18-46665492-C-T

Variant names:

• chr18-46665492-C-T
• rs430374
• XR_935430.4:n.716G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_935430.4(LOC105372096):​n.716G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 152,014 control chromosomes in the GnomAD database, including 4,637 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.24 (4637 hom., cov: 31)
• Consequence: LOC105372096 XR_935430.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152
• Publications: 3 publications found

Genes affected

LOC105372096 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372096	XR_935430.4	n.716G>A		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36649 AN: 151896 Hom.: 4637 Cov.: 31

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.243

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.241 AC: 36665 AN: 152014 Hom.: 4637 Cov.: 31 AF XY: 0.240 AC XY: 17864 AN XY: 74306

African (AFR) AF: 0.199 AC: 8238 AN: 41470

American (AMR) AF: 0.194 AC: 2968 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1159 AN: 3468

East Asian (EAS) AF: 0.133 AC: 687 AN: 5164

South Asian (SAS) AF: 0.113 AC: 543 AN: 4822

European-Finnish (FIN) AF: 0.333 AC: 3510 AN: 10548

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18783 AN: 67964

Other (OTH) AF: 0.240 AC: 506 AN: 2108

Alfa AF: 0.258 Hom.: 16390

Bravo AF: 0.231

Asia WGS AF: 0.120 AC: 420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.4
DANN	Benign	0.73
PhyloP100		0.15

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs430374; hg19: chr18-44245455;